# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am

# Copyright (C) 1994, 1995-8, 1999, 2001 Free Software Foundation, Inc.
# This Makefile.in is free software; the Free Software Foundation
# gives unlimited permission to copy and/or distribute it,
# with or without modifications, as long as this notice is preserved.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.


SHELL = @SHELL@

srcdir = @srcdir@
top_srcdir = @top_srcdir@
VPATH = @srcdir@
prefix = @prefix@
exec_prefix = @exec_prefix@

bindir = @bindir@
sbindir = @sbindir@
libexecdir = @libexecdir@
datadir = @datadir@
sysconfdir = @sysconfdir@
sharedstatedir = @sharedstatedir@
localstatedir = @localstatedir@
libdir = @libdir@
infodir = @infodir@
mandir = @mandir@
includedir = @includedir@
oldincludedir = /usr/include

DESTDIR =

pkgdatadir = $(datadir)/@PACKAGE@
pkglibdir = $(libdir)/@PACKAGE@
pkgincludedir = $(includedir)/@PACKAGE@

top_builddir = ..

ACLOCAL = @ACLOCAL@
AUTOCONF = @AUTOCONF@
AUTOMAKE = @AUTOMAKE@
AUTOHEADER = @AUTOHEADER@

INSTALL = @INSTALL@
INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
INSTALL_DATA = @INSTALL_DATA@
INSTALL_SCRIPT = @INSTALL_SCRIPT@
transform = @program_transform_name@

NORMAL_INSTALL = :
PRE_INSTALL = :
POST_INSTALL = :
NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
host_alias = @host_alias@
host_triplet = @host@
CC = @CC@
HAVE_LIB = @HAVE_LIB@
LIB = @LIB@
LTLIB = @LTLIB@
MAKEINFO = @MAKEINFO@
PACKAGE = @PACKAGE@
VERSION = @VERSION@

bin_PROGRAMS = variscan
variscan_SOURCES = variscan.c variscan.h 			statistics.c statistics.h 			common.c common.h 			linefile.c linefile.h 			memalloc.c memalloc.h 			dlist.c dlist.h 			errabort.c errabort.h 			dystring.c dystring.h 			intExp.c kxTok.h kxTok.c 			pop.c pop.h 			window.c window.h 			free.c free.h 			output.c output.h 			readphylip.c readphylip.h 			readaxt.c readaxt.h 			readmga.c readmga.h 			readmaf.c readmaf.h 			readhapmap.c readhapmap.h 			readxmfa.c readxmfa.h 			readmav.c readmav.h 			ran1.c ran1.h 			swcolumn.c swcolumn.h 			swnet.c swnet.h 			swpoly.c swpoly.h 			swref.c swref.h

# 			globalslinux.c globalslinux.h globalswin32.c globalswin32.h 
variscan_LDFLAGS = -lm
#AM_CPPFLAGS = -DVARISCAN -lm
AM_CPPFLAGS = -DVARISCAN
# AM_CFLAGS =
@DEBUG_TRUE@OTHERFLAGS = -g -pg -fprofile-arcs -ftest-coverage -ftrapv
@DEBUG_FALSE@OTHERFLAGS = -DNDEBUG -O3
# coverage -> -fprofile-arcs -ftest-coverage
# AM_CFLAGS =
# AM_LDFLAGS =   $(OTHERFLAGS) -Wall -lm -ansi

#AM_CFLAGS = $(OTHERFLAGS) -W -Wall -lm -ansi 
AM_CFLAGS = $(OTHERFLAGS) -W -Wall -ansi -pedantic
CFLAGS = 
mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
CONFIG_CLEAN_FILES = 
PROGRAMS =  $(bin_PROGRAMS)


DEFS = @DEFS@ -I. -I$(srcdir) 
CPPFLAGS = @CPPFLAGS@
LDFLAGS = @LDFLAGS@
LIBS = @LIBS@
variscan_OBJECTS =  variscan.o statistics.o common.o linefile.o \
memalloc.o dlist.o errabort.o dystring.o intExp.o kxTok.o pop.o \
window.o free.o output.o readphylip.o readaxt.o readmga.o readmaf.o \
readhapmap.o readxmfa.o readmav.o ran1.o swcolumn.o swnet.o swpoly.o \
swref.o
variscan_LDADD = $(LDADD)
variscan_DEPENDENCIES = 
COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
DIST_COMMON =  Makefile.am Makefile.in


DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)

TAR = tar
GZIP_ENV = --best
DEP_FILES =  .deps/common.P .deps/dlist.P .deps/dystring.P \
.deps/errabort.P .deps/free.P .deps/intExp.P .deps/kxTok.P \
.deps/linefile.P .deps/memalloc.P .deps/output.P .deps/pop.P \
.deps/ran1.P .deps/readaxt.P .deps/readhapmap.P .deps/readmaf.P \
.deps/readmav.P .deps/readmga.P .deps/readphylip.P .deps/readxmfa.P \
.deps/statistics.P .deps/swcolumn.P .deps/swnet.P .deps/swpoly.P \
.deps/swref.P .deps/variscan.P .deps/window.P
SOURCES = $(variscan_SOURCES)
OBJECTS = $(variscan_OBJECTS)

all: all-redirect
.SUFFIXES:
.SUFFIXES: .S .c .o .s
$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4) 
	cd $(top_srcdir) && $(AUTOMAKE) --gnu src/Makefile

Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status $(BUILT_SOURCES)
	cd $(top_builddir) \
	  && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status


mostlyclean-binPROGRAMS:

clean-binPROGRAMS:
	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)

distclean-binPROGRAMS:

maintainer-clean-binPROGRAMS:

install-binPROGRAMS: $(bin_PROGRAMS)
	@$(NORMAL_INSTALL)
	$(mkinstalldirs) $(DESTDIR)$(bindir)
	@list='$(bin_PROGRAMS)'; for p in $$list; do \
	  if test -f $$p; then \
	    echo "  $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \
	     $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
	  else :; fi; \
	done

uninstall-binPROGRAMS:
	@$(NORMAL_UNINSTALL)
	list='$(bin_PROGRAMS)'; for p in $$list; do \
	  rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \
	done

.s.o:
	$(COMPILE) -c $<

.S.o:
	$(COMPILE) -c $<

mostlyclean-compile:
	-rm -f *.o core *.core

clean-compile:

distclean-compile:
	-rm -f *.tab.c

maintainer-clean-compile:

variscan: $(variscan_OBJECTS) $(variscan_DEPENDENCIES)
	@rm -f variscan
	$(LINK) $(variscan_LDFLAGS) $(variscan_OBJECTS) $(variscan_LDADD) $(LIBS)

tags: TAGS

ID: $(HEADERS) $(SOURCES) $(LISP)
	list='$(SOURCES) $(HEADERS)'; \
	unique=`for i in $$list; do echo $$i; done | \
	  awk '    { files[$$0] = 1; } \
	       END { for (i in files) print i; }'`; \
	here=`pwd` && cd $(srcdir) \
	  && mkid -f$$here/ID $$unique $(LISP)

TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) $(LISP)
	tags=; \
	here=`pwd`; \
	list='$(SOURCES) $(HEADERS)'; \
	unique=`for i in $$list; do echo $$i; done | \
	  awk '    { files[$$0] = 1; } \
	       END { for (i in files) print i; }'`; \
	test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
	  || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags  $$unique $(LISP))

mostlyclean-tags:

clean-tags:

distclean-tags:
	-rm -f TAGS ID

maintainer-clean-tags:

distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)

subdir = src

distdir: $(DISTFILES)
	here=`cd $(top_builddir) && pwd`; \
	top_distdir=`cd $(top_distdir) && pwd`; \
	distdir=`cd $(distdir) && pwd`; \
	cd $(top_srcdir) \
	  && $(AUTOMAKE) --include-deps --build-dir=$$here --srcdir-name=$(top_srcdir) --output-dir=$$top_distdir --gnu src/Makefile
	@for file in $(DISTFILES); do \
	  d=$(srcdir); \
	  if test -d $$d/$$file; then \
	    cp -pr $$d/$$file $(distdir)/$$file; \
	  else \
	    test -f $(distdir)/$$file \
	    || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
	    || cp -p $$d/$$file $(distdir)/$$file || :; \
	  fi; \
	done

DEPS_MAGIC := $(shell mkdir .deps > /dev/null 2>&1 || :)

-include $(DEP_FILES)

mostlyclean-depend:

clean-depend:

distclean-depend:
	-rm -rf .deps

maintainer-clean-depend:

%.o: %.c
	@echo '$(COMPILE) -c $<'; \
	$(COMPILE) -Wp,-MD,.deps/$(*F).pp -c $<
	@-cp .deps/$(*F).pp .deps/$(*F).P; \
	tr ' ' '\012' < .deps/$(*F).pp \
	  | sed -e 's/^\\$$//' -e '/^$$/ d' -e '/:$$/ d' -e 's/$$/ :/' \
	    >> .deps/$(*F).P; \
	rm .deps/$(*F).pp

%.lo: %.c
	@echo '$(LTCOMPILE) -c $<'; \
	$(LTCOMPILE) -Wp,-MD,.deps/$(*F).pp -c $<
	@-sed -e 's/^\([^:]*\)\.o[ 	]*:/\1.lo \1.o :/' \
	  < .deps/$(*F).pp > .deps/$(*F).P; \
	tr ' ' '\012' < .deps/$(*F).pp \
	  | sed -e 's/^\\$$//' -e '/^$$/ d' -e '/:$$/ d' -e 's/$$/ :/' \
	    >> .deps/$(*F).P; \
	rm -f .deps/$(*F).pp
info-am:
info: info-am
dvi-am:
dvi: dvi-am
check-am: all-am
check: check-am
installcheck-am:
installcheck: installcheck-am
install-exec-am: install-binPROGRAMS
install-exec: install-exec-am

install-data-am:
install-data: install-data-am

install-am: all-am
	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
install: install-am
uninstall-am: uninstall-binPROGRAMS
uninstall: uninstall-am
all-am: Makefile $(PROGRAMS)
all-redirect: all-am
install-strip:
	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
installdirs:
	$(mkinstalldirs)  $(DESTDIR)$(bindir)


mostlyclean-generic:

clean-generic:

distclean-generic:
	-rm -f Makefile $(CONFIG_CLEAN_FILES)
	-rm -f config.cache config.log stamp-h stamp-h[0-9]*

maintainer-clean-generic:
mostlyclean-am:  mostlyclean-binPROGRAMS mostlyclean-compile \
		mostlyclean-tags mostlyclean-depend mostlyclean-generic

mostlyclean: mostlyclean-am

clean-am:  clean-binPROGRAMS clean-compile clean-tags clean-depend \
		clean-generic mostlyclean-am

clean: clean-am

distclean-am:  distclean-binPROGRAMS distclean-compile distclean-tags \
		distclean-depend distclean-generic clean-am

distclean: distclean-am

maintainer-clean-am:  maintainer-clean-binPROGRAMS \
		maintainer-clean-compile maintainer-clean-tags \
		maintainer-clean-depend maintainer-clean-generic \
		distclean-am
	@echo "This command is intended for maintainers to use;"
	@echo "it deletes files that may require special tools to rebuild."

maintainer-clean: maintainer-clean-am

.PHONY: mostlyclean-binPROGRAMS distclean-binPROGRAMS clean-binPROGRAMS \
maintainer-clean-binPROGRAMS uninstall-binPROGRAMS install-binPROGRAMS \
mostlyclean-compile distclean-compile clean-compile \
maintainer-clean-compile tags mostlyclean-tags distclean-tags \
clean-tags maintainer-clean-tags distdir mostlyclean-depend \
distclean-depend clean-depend maintainer-clean-depend info-am info \
dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
install-exec install-data-am install-data install-am install \
uninstall-am uninstall all-redirect all-am all installdirs \
mostlyclean-generic distclean-generic clean-generic \
maintainer-clean-generic clean mostlyclean distclean maintainer-clean

			globalslinux.c globalslinux.h

# bin_PROGRAMS= axt_variscan
# axt_variscan_SOURCES = variscan.20040128.c variscan.20040128.h statistics.c statistics.h intExp.c kxTok.h kxTok.c common.c common.h linefile.c linefile.h memalloc.c memalloc.h dlist.c dlist.h errabort.c errabort.h dystring.c dystring.h pop.c pop.h
# AM_CPPFLAGS = -DAXT_VARISCAN
# # AM_CFLAGS = -pg
# AM_LDFLAGS = -lm

# bin_PROGRAMS= _test_free_polyarray
# _test_free_polyarray_SOURCES = _test_free_polyarray.c variscan.20040128.c variscan.20040128.h statistics.c statistics.h intExp.c kxTok.h kxTok.c common.c common.h linefile.c linefile.h memalloc.c memalloc.h dlist.c dlist.h errabort.c errabort.h dystring.c dystring.h 
# # AM_CPPFLAGS = -DAXT_VARISCAN
# # AM_CFLAGS = -pg
# AM_LDFLAGS = -lm

# bin_PROGRAMS= __prova_dl
# __prova_dl_SOURCES = _prova_dl.c variscan.h common.c common.h linefile.c \
# 			linefile.h memalloc.c memalloc.h dlist.c \
# 			dlist.h errabort.c errabort.h dystring.c dystring.h
# # AM_CFLAGS = -DVARISCAN -pg

# bin_PROGRAMS= prova_borrar
# prova_borrar_SOURCES = prova_borrar.c common.c common.h linefile.c	\
# 			  linefile.h memalloc.c memalloc.h errabort.c errabort.h dlist.c dlist.h

# # AM_CFLAGS = -DMGAALN2PHY
# CFLAGS = -g -pg

# bin_PROGRAMS= provadystringlist
# provadystringlist_SOURCES = provadystringlist.c common.c common.h linefile.c \
# 			  linefile.h memalloc.c memalloc.h dlist.c \
# 			  dlist.h errabort.c errabort.h dystring.c dystring.h
# AM_CFLAGS =
# CFLAGS = -g -pg

# bin_PROGRAMS= variscanmgaaln2phy
# variscanmgaaln2phy_SOURCES = 20030526mgaaln2phy.c mgaaln2phy.h common.c common.h linefile.c \
# 			  linefile.h memalloc.c memalloc.h dlist.c \
# 			  dlist.h errabort.c errabort.h dystring.c dystring.h
# AM_CFLAGS = -DMGAALN2PHY
# CFLAGS = -g -pg

# bin_PROGRAMS= variscanmain
# variscanmain_SOURCES = main.c mga.h common.c common.h linefile.c \
# 			  linefile.h memalloc.c memalloc.h dlist.c \
# 			  dlist.h errabort.c errabort.h dystring.c dystring.h
# AM_CFLAGS = -DMAIN
# #CFLAGS = -g -pg -lm
# CFLAGS = -lm

# bin_PROGRAMS= variscan
# variscan_SOURCES = proves20030428.c common.c common.h linefile.c \
# 			  linefile.h memalloc.c memalloc.h dlist.c \
# 			  dlist.h errabort.c errabort.h dystring.c dystring.h
# AM_CFLAGS = -DMAIN
# CFLAGS = -g -pg -lm
# #CFLAGS = -lm

# bin_PROGRAMS= borrar3
# borrar3_SOURCES = borrar3.c
# AM_CFLAGS = 
# CFLAGS = -g -lm -pg

# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
